MolNFT v1 · #108165 · protein
N-terminal bromodomain of human BRD2 with 1-((2R,4S)-2-methyl-4- (phenylamino)-6-(4-(piperidin-1-YLMETHYL)PHENYL)-3,4-dihydroquinolin- 1(2H)-YL)ETHANONE
4UYH · Bromodomain-containing protein 2: “N-terminal bromodomain of human BRD2 with 1-((2R,4S)-2-methyl-4…”. X-ray diffraction, 2 ligands (9S3, SO4), 7 pockets (best druggability 0.66). MolNFT v1 #108165 on GenesisL1: 3D structure, binding…
- PDB
- 4UYH
- Type
- protein
- Length
- 321 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- 9S3, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 109 | 64% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 107 | 64% helix, 0% strand | P25440 |
| C | Bromodomain-containing protein 2 | protein | 105 | 63% helix, 0% strand | P25440 |
Ligands and binding sites
- 9S3 · 1-[(2S,4R)-2-methyl-4-(phenylamino)-6-[4-(piperidin-1-ylmethyl)phenyl]-3,4-dihydroquinolin-1(2H)-yl]ethanone · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.66 | 0.80 | 38 | DMS |
| 2 | 108 | 0.52 | 0.82 | 20 | 9S3 |
| 3 | 95 | 0.51 | 0.82 | 19 | 9S3 |
| 4 | 67 | 0.36 | 0.78 | 14 | empty |
| 5 | 87 | 0.35 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1068 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UYH · N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-((2R,4S)-2-methyl-4-(phenylamino)-6-(4-(piperi… · the same entry in another collection · chain A against A, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P25440
- Elsewhere: RCSB PDB 4UYH · PDBe 4UYH · UniProt P25440
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